The baby's father, alleged that staff at the community health centre in Jaisalmer's Ramgarh didn't inform him about the botch-up.
During the time of the delivery, the nurse pulled the foetus so carelessly that it resulted in splitting the body of the baby into two parts.
Two male nurses are the subject of controversy in India involving a baby who got decapitated while being born, as his head was left inside the mother's womb.
The horrifying incident occurred on Monday at Ramgarh primary health centre (PHC) in Jaisalmer.
The man in charge of the heath centre in Ramgargh, Dr Nikhil Sharma, said he wasn't present at the time of the incident.
A newborn's body was split into two while it was being pulled out with much force during delivery, a leading daily reported.
On Wednesday, a case was filed under IPC sections 304 A (causing death by negligence) and 336 (act endangering life or personal safety) against the two staffers of Ramgarh PHC. She was then sent to Jodhpur in a serious condition.
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A nurse pulled out the newborn with vast force during the delivery, the parents alleged.
After the incident, they asked family members to take the woman to Jaisalmer claiming that the opening of the womb had closed and it was hard to take the umbilical cord out. He led the police to the spot where he had hidden the torso.
When a team of doctors operated on the woman again, they were shocked to find the baby's head is in the womb.
Dr Usha Duggad, principal medical officer at Jawahar government hospital said it was a rare case.
Mr Bhati alleged that the nurses at the Ramgarh centre were drunk. The baby was half out when the pregnant woman was brought to the PHC.
Health department officials said a probe is on.